Protected cropping utilizing hydroponic systems are particularly vulnerable to the impacts of waterborne diseases which result in substantial crop damage and yield loss. This study assessed the potential of a citronella, red thyme, and clove bud essential oil blend (EOB) for plant safety, and pesticidal and antimicrobial activities. Results within model systems identified efficacy of EOB against aphids (p < 0.001), spider mites (p < 0.001), and fungus gnats (p < 0.001), and 250-fold diluted EOB against Pythium (p < 0.001), Phytophthora (p = 0.001), and Fusarium (p < 0.001). The plant safety trial indicated no impacts of 250-fold diluted EOB to capsicum health and glasshouse experiments demonstrated both curative and preventative efficacies against Pythium, based on reductions in the incidence and severity of infection. These results highlight the potential for the utilization of biopesticides for the effective and environmentally friendly management of common pests and diseases within hydroponic crop systems.